java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmPbBoundaryDetection

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmPbBoundaryDetection
extends AlgorithmBase
```
Compute probability of boundary using brightness gradient and texture gradient Original MATLAB code written by David R. Martin in April 2003 Reference: "Learning to Detect Natural Image Boundaries Using Local Brightness, Color, and Texture Cues" by David R. Martin, Charles C. Fowlkes, and Jitendra Malik, IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 26, No. 5, May, 2004, pp. 530-549.

Author:

ilb

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private static int`	`BG`
`private static int`	`BGTG`
`private byte[]`	`byteIntBuffer`	byte array for int *
`private byte[]`	`byteLongBuffer`	byte array for long *
`private byte[]`	`byteShortBuffer`	byte array for short *
`private static int`	`CANNY`
`private static int`	`CG`
`private static int`	`CGTG`
`private static int`	`COLOR_PRESENTATION`
`private double`	`epsilon`
`private static int`	`GM`
`private static int`	`GM2`
`private int`	`gradientType`
`private static int`	`GRAY_PRESENTATION`
`private double`	`highRadius`
`private double`	`hmult`
`private double`	`lowRadius`
`private int`	`nthresh`
`private int`	`numOrientations`
`private int`	`presentation`
`private java.io.RandomAccessFile`	`raFile`
`private double`	`sigma`
`private java.lang.String`	`smooth`
`private static int`	`TG`
`private static int`	`TWOMM`
`private static int`	`TWOMM2`
`private int`	`xDim`
`private int`	`yDim`

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmPbBoundaryDetection()`	AlgorithmPbBoundaryDetection - default constructor.
`AlgorithmPbBoundaryDetection(ModelImage destImg, ModelImage srcImg, int gradientType, int presentation, double lowRadius, double highRadius, int numOrientations, java.lang.String smooth, double sigma, int nthresh, double hmult)`	AlgorithmPbBoundaryDetection.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`assignTextons(int[][] map, double[][][][] fim, double[][] textons)`
`private void`	`cgmo(double[][][][] cg, double[] theta, ModelImage image, double[] radius, int numOrientations, int nbins, double sigmaSim, double gamma, java.lang.String smooth, double[] sigmaSmooth)`	cgmo for color Compute the color gradient at a single scale and multiple orientations
`private void`	`cgmo(double[][][][] cg, double[] theta, ModelImage image, double[] radius, int numOrientations, java.lang.String smooth, double[] sigmaSmooth)`
`private void`	`cgmo(double[][][] cg, double[] theta, ModelImage image, double radius, int numOrientations, int nbins, double sigmaSim, java.lang.String smooth, double sigmaSmooth)`	cgmo for black and white Compute the color gradient at a single scale and multiple orientations
`private void`	`cgmo(double[][][] cg, double[] theta, ModelImage image, double radius, int numOrientations, java.lang.String smooth, double sigmaSmooth)`
`private void`	`conv2(double[][] A, double[][] B, double[][] Cout)`
`private void`	`det2MM(double[][] e0, double[][] e1, double[][] theta, double sigmaI, double sigmaO)`
`private void`	`detBG(double[][][] bg, double[] theta)`
`private void`	`detBGTG(double[][][] bg, double[][][] tg, double[] theta)`
`private void`	`detCG(double[][][][] cg, double[] theta)`
`private void`	`detCGTG(double[][][][] cg, double[][][] tg, double[] theta)`
`private void`	`detGM(double[][] m, double[][] theta, double sigma)`
`private void`	`detTG(double[][][] tg, double[] theta)`
`private void`	`distsqr(double[][] z, double[][] x, double[][] y)`
`private void`	`fbRun(double[][][][] fim, double[][][][] fb, double[][] im)`
`private void`	`fbRun(double[][] fim, double[][] fb, double[][] im)`
`private void`	`fftconv2(double[][] fim, double[][] im, double[][] f)`
`private void`	`fitparab(double[][] a, double[][] b, double[][] c, double[][] z, double ra, double rb, double theta)`
`int`	`getInt(boolean bigEndian)`	Reads four signed bytes from file.
`long`	`getLong(boolean bigEndian)`	Reads eight unsigned bytes from file.
`java.lang.String`	`getString(int length)`	Reads a string from a file of given `length`.
`int`	`getUnsignedShort(boolean bigEndian)`	Reads two unsigned bytes from file.
`private void`	`nonmax(double[][] imout, double[][] im, double theta)`
`private void`	`nonmax(double[][] imout, double[][] im, double[][] theta)`
`private void`	`oeFilter(double[][] f, double sigmaX, double sigmaY, int support)`
`private void`	`oeFilter(double[][] f, double sigmaX, double sigmaY, int support, double theta)`
`private void`	`oeFilter(double[][] f, double sigmaX, double sigmaY, int support, double theta, int deriv)`
`private void`	`oeFilter(double[][] f, double sigmaX, double sigmaY, int support, double theta, int deriv, boolean dohil, boolean dovis)`	Compute unit L1- norm 2D filter.
`private void`	`padReflect(double[][] impad, double[][] im, int r)`
`private void`	`pb2MM(double[][] pb, double[][] theta)`
`private void`	`pb2MM2(double[][] pb, double[][] theta)`
`private void`	`pbBG(double[][] pb, double[][] theta)`
`private void`	`pbBGTG(double[][] pb, double[][] theta)`
`private void`	`pbCanny(double[][] pb)`
`private void`	`pbCG(double[][] pb, double[][] theta)`
`private void`	`pbCGTG(double[][] pb, double[][] theta)`
`private void`	`pbGM(double[][] pb, double[][] theta)`
`private void`	`pbGM2(double[][] pb, double[][] theta)`
`private void`	`pbTG(double[][] pb, double[][] theta)`
`private java.lang.String`	`readCString()`
`private void`	`readFile(double[][][][] fb, double[][] tex, double[][] tsim)`
`private void`	`RGB2Lab(double[][][] L, double[] red, double[] green, double[] blue)`
`void`	`runAlgorithm()`	Actually runs the algorithm.
`private void`	`savgol(double[][] c, double[][] z, int d, int k, double ra, double rb, double theta)`
`private void`	`tgmo(double[][][] tg, double[] theta, int[][] tmap, int ntex, double radius, int numOrientations, double[][] tsim, java.lang.String smooth, double sigma)`	Compute the texture gradient at a single scale and multiple orientations
`private void`	`tgso(double[][] tg, int[][] tmap, int ntex, double radius, double theta, java.lang.String smooth, double sigma, double[][] tsim)`	Compute the texture graident at a single orientation and scale

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

BGTG
```
private static final int BGTG
```
See Also:

Constant Field Values

CGTG
```
private static final int CGTG
```
See Also:

Constant Field Values

BG
```
private static final int BG
```
See Also:

Constant Field Values

CG
```
private static final int CG
```
See Also:

Constant Field Values

TG
```
private static final int TG
```
See Also:

Constant Field Values

GM
```
private static final int GM
```
See Also:

Constant Field Values

GM2
```
private static final int GM2
```
See Also:

Constant Field Values

TWOMM
```
private static final int TWOMM
```
See Also:

Constant Field Values

TWOMM2
```
private static final int TWOMM2
```
See Also:

Constant Field Values

CANNY
```
private static final int CANNY
```
See Also:

Constant Field Values

gradientType
```
private int gradientType
```

GRAY_PRESENTATION
```
private static final int GRAY_PRESENTATION
```
See Also:

Constant Field Values

COLOR_PRESENTATION
```
private static final int COLOR_PRESENTATION
```
See Also:

Constant Field Values

presentation
```
private int presentation
```

lowRadius
```
private double lowRadius
```

highRadius
```
private double highRadius
```

numOrientations
```
private int numOrientations
```

smooth
```
private java.lang.String smooth
```

sigma
```
private double sigma
```

nthresh
```
private int nthresh
```

hmult
```
private double hmult
```

xDim
```
private int xDim
```

yDim
```
private int yDim
```

raFile

private java.io.RandomAccessFile raFile

byteShortBuffer
```
private final byte[] byteShortBuffer
```
byte array for short *

byteIntBuffer
```
private final byte[] byteIntBuffer
```
byte array for int *

byteLongBuffer
```
private final byte[] byteLongBuffer
```
byte array for long *

epsilon
```
private final double epsilon
```

Constructor Detail

AlgorithmPbBoundaryDetection
```
public AlgorithmPbBoundaryDetection()
```
AlgorithmPbBoundaryDetection - default constructor.

AlgorithmPbBoundaryDetection

public AlgorithmPbBoundaryDetection(ModelImage destImg,
                                    ModelImage srcImg,
                                    int gradientType,
                                    int presentation,
                                    double lowRadius,
                                    double highRadius,
                                    int numOrientations,
                                    java.lang.String smooth,
                                    double sigma,
                                    int nthresh,
                                    double hmult)

AlgorithmPbBoundaryDetection.

Parameters:: destImg - DOCUMENT ME!; srcImg - DOCUMENT ME!; gradientType -; presentation -; lowRadius -; highRadius -; numOrientations -; smooth -; sigma -

Method Detail

runAlgorithm
```
public void runAlgorithm()
```
Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

pbCanny

private void pbCanny(double[][] pb)

pb2MM2

private void pb2MM2(double[][] pb,
                    double[][] theta)

pb2MM

private void pb2MM(double[][] pb,
                   double[][] theta)

pbCG

private void pbCG(double[][] pb,
                  double[][] theta)

pbCGTG

private void pbCGTG(double[][] pb,
                    double[][] theta)

pbGM2

private void pbGM2(double[][] pb,
                   double[][] theta)

pbGM

private void pbGM(double[][] pb,
                  double[][] theta)

pbBG

private void pbBG(double[][] pb,
                  double[][] theta)

pbBGTG

private void pbBGTG(double[][] pb,
                    double[][] theta)

pbTG

private void pbTG(double[][] pb,
                  double[][] theta)

nonmax

private void nonmax(double[][] imout,
                    double[][] im,
                    double[][] theta)

nonmax

private void nonmax(double[][] imout,
                    double[][] im,
                    double theta)

det2MM
```
private void det2MM(double[][] e0,
                    double[][] e1,
                    double[][] theta,
                    double sigmaI,
                    double sigmaO)
```
Parameters:

e0 - output smaller eigenvlaues

e1 - output larger eigenvalues

theta - output Orientation of first eigenvector + PI/2 (i.e. orientation of possible edge)

sigmaI - input Inner scale (sigma for image derivatives)

sigmaO - input Outer scale (sigma for spatial averaging)

detCG

private void detCG(double[][][][] cg,
                   double[] theta)

detCGTG

private void detCGTG(double[][][][] cg,
                     double[][][] tg,
                     double[] theta)

detGM

private void detGM(double[][] m,
                   double[][] theta,
                   double sigma)

detBG

private void detBG(double[][][] bg,
                   double[] theta)

detBGTG

private void detBGTG(double[][][] bg,
                     double[][][] tg,
                     double[] theta)

detTG

private void detTG(double[][][] tg,
                   double[] theta)

assignTextons

private void assignTextons(int[][] map,
                           double[][][][] fim,
                           double[][] textons)

distsqr

private void distsqr(double[][] z,
                     double[][] x,
                     double[][] y)

readFile

private void readFile(double[][][][] fb,
                      double[][] tex,
                      double[][] tsim)

getString
```
public final java.lang.String getString(int length)
                                 throws java.io.IOException
```
Reads a string from a file of given length.

Parameters:

length - Number of bytes that form the string.

Returns:

The string read from the file.

Throws:

java.io.IOException - if there is an error reading the file

getLong
```
public final long getLong(boolean bigEndian)
                   throws java.io.IOException
```
Reads eight unsigned bytes from file.

Parameters:

bigEndian - true indicates big endian byte order, false indicates little endian.

Returns:

The value of the long read from the file.

Throws:

java.io.IOException - if there is an error reading the file

getInt
```
public final int getInt(boolean bigEndian)
                 throws java.io.IOException
```
Reads four signed bytes from file.

Parameters:

bigEndian - true indicates big endian byte order, false indicates little endian.

Returns:

The value of the integer read from the file.

Throws:

java.io.IOException - if there is an error reading the file

getUnsignedShort
```
public final int getUnsignedShort(boolean bigEndian)
                           throws java.io.IOException
```
Reads two unsigned bytes from file.

Parameters:

bigEndian - true indicates big endian byte order, false indicates little endian.

Returns:

The value of unsigned short read from the file returned as an int.

Throws:

java.io.IOException - if there is an error reading the file

readCString

private java.lang.String readCString()
                              throws java.io.IOException

Throws:: java.io.IOException

cgmo

private void cgmo(double[][][][] cg,
                  double[] theta,
                  ModelImage image,
                  double[] radius,
                  int numOrientations,
                  java.lang.String smooth,
                  double[] sigmaSmooth)

cgmo
```
private void cgmo(double[][][][] cg,
                  double[] theta,
                  ModelImage image,
                  double[] radius,
                  int numOrientations,
                  int nbins,
                  double sigmaSim,
                  double gamma,
                  java.lang.String smooth,
                  double[] sigmaSmooth)
```
cgmo for color Compute the color gradient at a single scale and multiple orientations

Parameters:

cg - output output [yDim][xDim][3][numOrientations] array for color

output - [numOrientations] theta

image - RGB image, values in [0, 1].

radius - Radius of disc for cg array

numOrientations - Number of orientations for cg array

nbins - Number of bins; should be > 1/sigmaSim.

sigmaSim - For color similarity function

gamma - Gamma correction for LAB [2.5].

smooth - Smoothing method, one of {"gaussian", "savgol", "none"}, default none

sigmaSmooth - Sigma for smoothing, default to radius

RGB2Lab

private void RGB2Lab(double[][][] L,
                     double[] red,
                     double[] green,
                     double[] blue)

cgmo

private void cgmo(double[][][] cg,
                  double[] theta,
                  ModelImage image,
                  double radius,
                  int numOrientations,
                  java.lang.String smooth,
                  double sigmaSmooth)

cgmo
```
private void cgmo(double[][][] cg,
                  double[] theta,
                  ModelImage image,
                  double radius,
                  int numOrientations,
                  int nbins,
                  double sigmaSim,
                  java.lang.String smooth,
                  double sigmaSmooth)
```
cgmo for black and white Compute the color gradient at a single scale and multiple orientations

Parameters:

cg - output [yDim][xDim][numOrientations] array for black and white

output - [numOrientations] theta

image - Grayscale image, values in [0, 1].

radius - Radius of disc for cg array

numOrientations - Number of orientations for cg array

nbins - Number of bins; should be > 1/sigmaSim.

sigmaSim - For color similarity function

smooth - Smoothing method, one of {"gaussian", "savgol", "none"}, default none

sigmaSmooth - Sigma for smoothing, default to radius

tgmo
```
private void tgmo(double[][][] tg,
                  double[] theta,
                  int[][] tmap,
                  int ntex,
                  double radius,
                  int numOrientations,
                  double[][] tsim,
                  java.lang.String smooth,
                  double sigma)
```
Compute the texture gradient at a single scale and multiple orientations

Parameters:

output - tg [yDim][xDim][numOrientations] array

output - [numOrientations] theta Disc orientations (which are orthogonal to the texture gradient).

tmap - [yDim][xDim] Texton map, values in [1, ntex]

ntex - Number of textons

radius - Radius of disc for texture gradient

numOrientations - Number of orientations at which to compute the texture graident

tsim - Texton similarity matrix. If not provided, then use chi-squared.

smooth - Smoothing method. One of "gaussian", "savgol", "none". Default "none".

sigma - Sigma for smoothing. Default to radius.

tgso
```
private void tgso(double[][] tg,
                  int[][] tmap,
                  int ntex,
                  double radius,
                  double theta,
                  java.lang.String smooth,
                  double sigma,
                  double[][] tsim)
```
Compute the texture graident at a single orientation and scale

Parameters:

output - tg [yDim][xDim] array

tmap - [yDim][xDim] Texton map, values in [1, ntex].

ntex - Number of textons

radius - Radius of disc for tg

theta - Orientation orthogonal to tg.

smooth - Smoothing method, one of {"gaussian", "savgol", "none"}, default = "none".

sigma - Sigma for smoothing. Default to radius.

tsim - [ntex][ntex] Texton similarity matrix. If not provided, then use chi-squared.

fitparab

private void fitparab(double[][] a,
                      double[][] b,
                      double[][] c,
                      double[][] z,
                      double ra,
                      double rb,
                      double theta)

savgol

private void savgol(double[][] c,
                    double[][] z,
                    int d,
                    int k,
                    double ra,
                    double rb,
                    double theta)

fbRun

private void fbRun(double[][][][] fim,
                   double[][][][] fb,
                   double[][] im)

fbRun

private void fbRun(double[][] fim,
                   double[][] fb,
                   double[][] im)

fftconv2

private void fftconv2(double[][] fim,
                      double[][] im,
                      double[][] f)

padReflect

private void padReflect(double[][] impad,
                        double[][] im,
                        int r)

oeFilter

private void oeFilter(double[][] f,
                      double sigmaX,
                      double sigmaY,
                      int support)

oeFilter

private void oeFilter(double[][] f,
                      double sigmaX,
                      double sigmaY,
                      int support,
                      double theta)

oeFilter

private void oeFilter(double[][] f,
                      double sigmaX,
                      double sigmaY,
                      int support,
                      double theta,
                      int deriv)

oeFilter
```
private void oeFilter(double[][] f,
                      double sigmaX,
                      double sigmaY,
                      int support,
                      double theta,
                      int deriv,
                      boolean dohil,
                      boolean dovis)
```
Compute unit L1- norm 2D filter. The filter is a Gaussian in the x direction The filter is a Gaussian derivative with optional Hilbert transform in the y direction. The filter is zero-meaned if deriv > 0.

Parameters:

f - output [sz][sz] square filter

sigmaX -

sigmaY -

support - Make filter +/- this many sigma

theta - Orientation of x axis, in radians

deriv - Degree of y derivative, one of {0, 1, 2}.

dohil - Do Hilbert transform in y direction?

dovis - Visualization for debugging?

conv2

private void conv2(double[][] A,
                   double[][] B,
                   double[][] Cout)

Class AlgorithmPbBoundaryDetection

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

BGTG

CGTG

BG

CG

TG

GM

GM2

TWOMM

TWOMM2

CANNY

gradientType

GRAY_PRESENTATION

COLOR_PRESENTATION

presentation

lowRadius

highRadius

numOrientations

smooth

sigma

nthresh

hmult

xDim

yDim

raFile

byteShortBuffer

byteIntBuffer

byteLongBuffer

epsilon

Constructor Detail

AlgorithmPbBoundaryDetection

AlgorithmPbBoundaryDetection

Method Detail

runAlgorithm

pbCanny

pb2MM2

pb2MM

pbCG

pbCGTG

pbGM2

pbGM

pbBG

pbBGTG

pbTG

nonmax

nonmax

det2MM

detCG

detCGTG

detGM

detBG

detBGTG

detTG

assignTextons

distsqr

readFile

getString

getLong

getInt

getUnsignedShort

readCString

cgmo

cgmo

RGB2Lab

cgmo

cgmo

tgmo

tgso

fitparab